January 27, 2012

The Arabian cradle (Fernandes et al. 2012)

I have written about Out-of-Arabia before. It is important to remember, when discussing the prehistory of Arabia in terms of the modern inhabitants, that the peninsula undergoes periods of extreme aridity followed by periods of relative humidity. Hence, unlike other regions of the world where continuous occupation can be argued due to a fairly stable climate, this is not the case for Arabia.

This observation is important because when looking at modern populations we cannot a priori assume the survival of the most ancient inhabitants. Nonetheless, it can be well argued that Homo sapiens is an extremely adaptable species: not only did it spread throughout the world in a geological blink of an eye over the last 50 thousand years or so, but also persisted throughout most of the world, coming to occupy nearly every corner of the planet.

So, even though hyper-arid periods may have driven away most people from desert areas, perhaps they did not drive away everybody. There may yet be relics of ancient populations to be found. This is exactly what a new paper proposes: that Arabia possesses extremely old mtDNA lineages within the major macro-haplogroup N, dating to about 60,000 years ago. This is quite close to the estimates time depth of haplogroup L3 which unites many Africans with the Eurasians belonging to macrohaplogroups M and N.

The mainstream understanding of what happened -according to most geneticists- is that modern humans began spreading from Africa at around that time, about 60-70 thousand years ago. On the contrary, archaeologists have found indisputable evidence (palaeoanthropological or archaeological) of modern humans in Asia from before 100 thousand years, stretching from the Levant to the southern parts of Arabia.

There are two possibilities:

The pre-70ka modern humans in Asia left absolutely no traces of mtDNA, and all of the extant mtDNA in Asia is derived from post-70ka Africans. Hence, the pre-70ka modern humans in Asia were the descendants of failed exodi.

The people who expanded post-70ka in Asia were descended from people who lived in Asia before 100ka, descendants of successful exodi perhaps associated with the Mount Carmel hominins or the recently discovered Nubian Complex.

I am rather in favor of the second hypothesis; the authors of the current paper favor the first. It seems unnatural that pre-70ka modern humans in Asia would just vanish: why would they? They, apparently, lived across a vast area, and were bearers of technologies that were no worse than contemporaneous African cultures. Moreover, there is simply no archaeological evidence about population movements originating in Africa at 70-60ka.

However, if the second hypothesis is true, there is a problem: haplogroup L3 is dated to 70ka, so if the expansion associated with it started in Asia, that means that there must have been substantial back-migration of L3-related lineages back to Africa. I don't see any major problem with that hypothesis, but it is true that many scientists are reluctant to feature extensive back-migration to Africa into their models. At present it has not been possible to determine to what extent genetic diversity in Africa is due to great antiquity vs. admixture of divergent human populations, which I have called Afrasian (related to Eurasians) and Palaeoafrican. If L3 did originate in Africa, then the concusion of a recent African exodus is inescapable.

The major contribution of the current paper is that it fixes a major human expansion Out-of-Arabia at very close to 60ka. Whether this expansion originated from transient Out-of-Africans who had recently exited Africa, or from long settled populations of Asia (prior to 100ka) remains to be seen.

From the paper:

The presence of archaeological sites in the Gulf basin demonstrates a long tradition of human occupation.9 However, neither direct cultural influences from the Levant nor any African influence has been detected in the Upper Palaeolithic (Late Pleistocene) lithics observed in eastern Arabia, pointing to a local development of cultural techniques.9,47 Curiously, however, the fact that some of the branches studied here include deep lineages in eastern Africa (haplogroups I, N1a, and N1f) shows that migration back to Africa occurred a number of times between 15 and 40 ka ago.

The hypothesized Gulf Oasis9 appears to be the most likely locus of the earliest branching of haplogroup N, including the three relict basal N(xR) haplogroups studied here, as well as the major Eurasian haplogroup R. Time estimates, frequencies, and genetic diversities reported here for these haplogroups are often similar between the Levant and Arabia, challenging the hypothesis of longterm isolation between these two regions. The other two refugia identified in the south and southwest of the Peninsula might have acted as a corridor for migrations west, back toward eastern Africa. Y chromosome microsatellite diversity in the Arabian Peninsula has suggested that Dubai and Oman share genetic affinities with other Near Eastern populations, whereas Saudi Arabia and Yemen show signs of greater isolation (although for fast-evolving microsatellites, these differences might reflect more recent events).4

The American Journal of Human Genetics, 26 January 2012 doi:10.1016/j.ajhg.2011.12.010

The Arabian Cradle: Mitochondrial Relicts of the First Steps along the Southern Route out of Africa

Verónica Fernandes et al.

A major unanswered question regarding the dispersal of modern humans around the world concerns the geographical site of the first human steps outside of Africa. The “southern coastal route” model predicts that the early stages of the dispersal took place when people crossed the Red Sea to southern Arabia, but genetic evidence has hitherto been tenuous. We have addressed this question by analyzing the three minor west-Eurasian haplogroups, N1, N2, and X. These lineages branch directly from the first non-African founder node, the root of haplogroup N, and coalesce to the time of the first successful movement of modern humans out of Africa, ∼60 thousand years (ka) ago. We sequenced complete mtDNA genomes from 85 Southwest Asian samples carrying these haplogroups and compared them with a database of 300 European examples. The results show that these minor haplogroups have a relict distribution that suggests an ancient ancestry within the Arabian Peninsula, and they most likely spread from the Gulf Oasis region toward the Near East and Europe during the pluvial period 55–24 ka ago. This pattern suggests that Arabia was indeed the first staging post in the spread of modern humans around the world.

A third possibility in addition to the two that you identify is that mtDNA based dates are miscalibrated or inaccurate and therefore understate the true age by something on the order of 50% in this era. Inaccuracies in demographic models used to generate the estimates (e.g. generation lengths that are too short, or effective population size estimates that are too large, or insufficent accounting for losses of new mutations in boom/bust population cycles), mutation rates in modern humans that are higher than longer range estimates from primates due to selective pressure arising from having a wider environmental niche, or other factors.

There is a 25,000 year gap in the Levantine modern human fossil record between the oldest modern human Out of Africa traces and the part of the modern human fossil record in the region that become continuous and other evidence of an Out of Africa event (i.e. basically from 100,000 BP to 75,000 BP), so there is some archaeological support for the failed exodus theory, and if the failed exodus theory is wrong, the time spent in a refuge was probably quite long (ca. 25,000 years +/-).

There is no especially good reason to privilege a Gulf Oasis, in particular, as a refugium (as opposed, e.g., to someplace else in West Asia or the Nile Basin), or to strongly suppose that the closest descendants of the refugia population(s) remain in the same geographic location as the original refuge. Migration of the refugium population is definitionally necessary in the case of a Gulf Oasis, and examples of exile/refugium populations that are mostly found in places distant from their place of origin (e.g. the Druze, the Jews, the Ket, the Apache, the Kordofans) are numerous. The geographic distribution of Y-DNA/mtDNA haplogroup phylogenies are, in any case, really a better fit to two separate refugiums appearing at or around the time of the first mutations making M and N distinct from L3, only one of which contributes to the founding population of West Eurasia when it expands (the N/R refuge), but both of which contribute to the founding population of East Eurasia when they expand (i.e. there is another M refuge and at the expansion point people from the N/R refuge admix with people from the M refuge).

There is also suggestive evidence from the distribution of private alleles in West Eurasia v. East Eurasia to support the argument that Neanderthal admixture happened in distinct parallel admixture events that were similar but separate in eve of expansion West Eurasian and eve of expansion East Eurasian populations at two different places within the Neanderthal range not long after moder humans expand out of these refugia (and prior to Denisovian admixture).

In contemporary populations, L3(x M, N) is most diverse in East Africa (http://4.bp.blogspot.com/-dl5eidKyyVI/TsVXES5X0mI/AAAAAAAAEUA/ZgBZjyOUd1Q/s1600/2011-11-17-184704_1366x768_scrot.png). In Arabia, it is clearly associated with relatively recent African gene flow. Arabia is otherwise dominated by M and N.

It is possible that L3 did originate in Arabia, and the only lineages that survived in Arabia share a more recent origin with Eurasians, whereas other basal clades migrated back to East Africa. However, I see no reason to view this possibility as the most likely scenario when it is evident that the OOA migrants spread shortly after the origin of L3, and L ultimately has an African origin. Furthermore, the dates for the various African L3(x M, N) subclades are rather similar to the dates for M and N.

I am not opposed to ancient back-migration into Africa. E could be the remnant of one such migration, as well as other more recent Eurasian clades that are present in East Africa. L3 is more of a stretch, in my opinion.

I agree with you that one has to be extremely cautious about the time estimates, and more likely than not, many are a factor of 2-3 off.

The authors are clearly bent to seek a Near East origin for as many subgroups they can loosely defend, even if that means that immediately adjacent nodes are primarily located either in Europe or in the Americas... And what's with the many glacial and late-glacial expansions - during the worst possible times?

Instead, we know as a fact expansions occurred ~130,000 to 105,000ya, ~45,000-35,000ya, and then again primarily post Younger Dryas. And perhaps any time 100,000 to 50,000ya in S/SE Asia, with the 70,000ya Toba interruption.

So, for example, X1 and X2 are dated at 21K and 22Kya, respectively, and X2a at 14.1 - with the origin of X1 and X2 postulated somewhere in the Near East/Caucasus region. Does anyone with a half-way intact mind really believe that these folks migrated from there into the Americas exactly during the height of the last ice age, also - neatly - not leaving any archeological nor genetic trace in between, and no autosomal or y-DNA connection, either?

Clearly, it makes more sense that X2 was already present in Siberia/Beringia ~40,000ya, and that many dates in the paper are a factor of two to three too young.

The "back" part is due to the fact that Africa has the deepest clades of the Y-chromosome and mtDNA phylogeny.

The "migration" part is argued primarily on the basis of Y-chromosomes. Within the CT clade, CF is clearly of Asian origin, whereas DE has split associations between Africa and Asia.

The origin of L3 in Africa is argued primarily on the _number_ of L3 sublineages that are found in Africa. In terms of age, the Asian branches of L3 (i.e., M and N) hold their own against the African ones. Moreover, we expect mtDNA diversity in Arabia to go through a severe bottleneck at least twice in the last 100k years. Moreover, I am completely reluctant to accept that the anatomically modern humans that lived in Asia from Israel to south Arabia >100ka left no mtDNA traces.

The lack of mtDNA traces is not so difficult to explain. The first paragraph of your blog post explains how they could have died out.

This is nothing extraordinary in human history. Despite the mixing that has taken place between modern humans and several archaic groups, no mtDNA traces of those archaics have ever been found. When considered with other lines of evidence, I do not understand why you will not acknowledge the clear possibility that the mtDNA of modern humans from Asia 100 kya could have died out.

This is nothing extraordinary in human history. Despite the mixing that has taken place between modern humans and several archaic groups, no mtDNA traces of those archaics have ever been found. When considered with other lines of evidence, I do not understand why you will not acknowledge the clear possibility that the mtDNA of modern humans from Asia 100 kya could have died out.

You are assuming that the entirety of the non-L3 part of the mtDNA phylogeny, going all the way back to mtDNA Eve, c. 200 thousand years ago was associated with anatomically modern humans.

That assumption is unwarranted, since the African palaeoanthropological record shows an entire series of populations with a mix of archaic and modern traits down to a few thousand years ago.

I see no reason to assume that mtDNA Eve, or her many daughters were anatomically modern humans. The fact that she was penecontemporaneous with the earliest anatomically modern fossils does not, in itself, indicate that either her or her many descendants were all AMH.

You are assuming that the entirety of the non-L3 part of the mtDNA phylogeny, going all the way back to mtDNA Eve, c. 200 thousand years ago was associated with anatomically modern humans.

That assumption is unwarranted, since the African palaeoanthropological record shows an entire series of populations with a mix of archaic and modern traits down to a few thousand years ago.

I see no reason to assume that mtDNA Eve, or her many daughters were anatomically modern humans. The fact that she was penecontemporaneous with the earliest anatomically modern fossils does not, in itself, indicate that either her or her many descendants were all AMH.

So you believe the very significant presence of the most divergent branches in the human mtDNA phylogeny among the Khoisan and Pygmies could be derived from archaic homo species?

I would say it is simply in accordance with the fact that their Y-DNA (mainly A and B) is most divergent in the human Y-DNA phylogeny. I highly doubt that these lineages are from archaic African humans. The anthropological record does show that archaic traits lived on until relatively recent times within Africa, however it also shows that they disappeared eventually as modern humans became dominant. Just a small part of their DNA appears to live on in modern Africans. This is quite similar to what happened when Neanderthals and Denisovans "vanished" in Eurasia as a result of the modern human expansion.

You are going to great lengths to protect the possibility that 100 kya Asian homo sapiens live on in modern Eurasians.

So you believe the very significant presence of the most divergent branches in the human mtDNA phylogeny among the Khoisan and Pygmies could be derived from archaic homo species?

Not only the Khoisan and Pygmies, and yes.

I would say it is simply in accordance with the fact that their Y-DNA (mainly A and B) is most divergent in the human Y-DNA phylogeny. I highly doubt that these lineages are from archaic African humans. The anthropological record does show that archaic traits lived on until relatively recent times within Africa, however it also shows that they disappeared eventually as modern humans became dominant. Just a small part of their DNA appears to live on in modern Africans. This is quite similar to what happened when Neanderthals and Denisovans "vanished" in Eurasia as a result of the modern human expansion.

On the contrary, the anthropological record does not show a gradual displacement of archaic by modern humans in Africa. In Eurasia this is the case: we first have Neandertals, Asian erectus, hobbits, etc. and by 17,000 years ago the last of those have disappeared. In Africa, the situation is quite different. If -as the standard model goes- modern humans originated in Africa 200,000 years, it is a real mystery why it took them 190,000 years to completely displace archaic humans, when it took only ~10,000 years in the case of Eurasia.

You are going to great lengths to protect the possibility that 100 kya Asian homo sapiens live on in modern Eurasians.

Anyone who thinks H. sapiens admixed with Neandertals in West Asia should also accept that they mixed with the much more related populations of H. sapiens that lived there, having exited pre-100ka.

It doesn't make much sense to simultaneously accept Neandertal admixture in Asia and deny "the possibility that 100 kya Asian homo sapiens live on in modern Eurasians." That would mean that the genes of Asian Neandertals survived, but of Asian sapiens did not, and I see no reason at all why that would be the case.

To clarify: The genes of Asian homo sapiens from 100 kya may have survived in Eurasians, but it seems that their mtDNA did not.On the contrary, the anthropological record does not show a gradual displacement of archaic by modern humans in Africa. In Eurasia this is the case: we first have Neandertals, Asian erectus, hobbits, etc. and by 17,000 years ago the last of those have disappeared. In Africa, the situation is quite different. If -as the standard model goes- modern humans originated in Africa 200,000 years, it is a real mystery why it took them 190,000 years to completely displace archaic humans, when it took only ~10,000 years in the case of Eurasia.

We know very little about the spread of modern humans in West-Central Africa. They may have spread relatively recently from other parts of Africa.

It doesn't make much sense to simultaneously accept Neandertal admixture in Asia and deny "the possibility that 100 kya Asian homo sapiens live on in modern Eurasians." That would mean that the genes of Asian Neandertals survived, but of Asian sapiens did not, and I see no reason at all why that would be the case.

You are assuming that the source of Eurasian Neanderthal ancestry is an admixture event with 100 kya Asian homo sapiens. Which is far from certain.

If this was truly the case, then I guess it took "Eurasians" more than 60,000 years to displace Neanderthals. That is about as logical as your suggestion that it took so long for "Africans" to displace African archaics.

"it is a real mystery why it took them 190,000 years to completely displace archaic humans, when it took only ~10,000 years in the case of Eurasia."

I couldn't comment on the main issue but...elephants.

http://www.sciencedaily.com/releases/2009/11/091127140706.htm

"Faith's findings support the idea that this mass extinction [in the Americas] was due to human overkill, comet impact or other rapid events rather than a slow attrition."

Maybe it took out of africa, adaptation to out of africa - including improvements to adaptability itself - and then a backflow to africa with that higher adaptability to displace the archaic humans within africa?

I see what you mean now. The 70 kya modern humans migrating Out of Africa may have mixed with the 100 kya folks (if they still existed, which is doubtful), but either way their mtDNA did not survive.

No, I don't believe there were 70kya modern humans migrating out of Africa. I am just pointing out that anyone who believes in such a migration and also believes in Neandertal admixture must also believe in admixture with pre-existing Homo sapiens populations in Asia. These populations cannot be dismissed as irrelevant Out-of-Africans that went bust anymore.

The 70 kya modern humans migrating Out of Africa may have mixed with the 100 kya folks...

Since the emergence of AMHs, 70kya was absolutely the worst of all times for any successful migration, from a climate viewpoint, until ~25-15kya. So, no - that didn't happen. OoAfrica and/or ooArabia clearly started earlier - and the archaeological record and SE Asian autosomal variation agree.

I was never opposed to the idea that they may have mixed with those modern humans. If they ever came into contact with them, that is. But their mtDNA (along with the mtDNA of Neanderthals and Denisovans) probably did not survive.

I was never opposed to the idea that they may have mixed with those modern humans. If they ever came into contact with them, that is. But their mtDNA (along with the mtDNA of Neanderthals and Denisovans) probably did not survive.

Currently assumed levels of Neandertal admixture are incompatible with the non-preservation of Neandertal mtDNA in modern humans:

So, those who think that modern humans exited Africa 70,000 years ago and mixed with _both_ Neandertals _and_ earlier Homo sapiens have their work cut out for them to explain away the complete disappearance of mtDNA from these populations. We must also add the Denisovans, as well as the archaic Africans.

A scenario which posits that humans admixed with all these different groups but received mtDNA from none of them is not plausible.

Since the emergence of AMHs, 70kya was absolutely the worst of all times for any successful migration, from a climate viewpoint, until ~25-15kya. So, no - that didn't happen. OoAfrica and/or ooArabia clearly started earlier - and the archaeological record and SE Asian autosomal variation agree.

A different stumbling block for the current Out-of-Africa thinking is that it posits that H. sapiens admixed with Neandertals in Eurasia much earlier than they did with archaic humans in Africa (estimated at ~36ky by Hammer et al.)

Why would modern humans wait ~150 thousand years to admix with archaic Africans in Africa itself, and start interbreeding with archaic Eurasians right away?

The problem is resolved if we consider that the admixture signal picked up by Hammer et al. corresponds to Homo sapiens entering Africa rather than the opposite: they didn't wait for 150 thousand years because they weren't around for 150 thousand years.

That would also explain the clear links of the Hofmeyr skull with Upper Paleolithic Eurasians, also from around the same age. Hofmeyr is unlike later and earlier populations from the same region.

A different stumbling block for the current Out-of-Africa thinking is that it posits that H. sapiens admixed with Neandertals in Eurasia much earlier than they did with archaic humans in Africa (estimated at ~36ky by Hammer et al.)

Why would modern humans wait ~150 thousand years to admix with archaic Africans in Africa itself, and start interbreeding with archaic Eurasians right away?

Hammer et al. only looked for signs of admixture with hominins that were more divergent from modern humans than Neanderthals. There is much more work to be done.

As I have already mentioned, we know very little about the ancient spread of modern humans in West-Central Africa. Hammer et al. found no signs of admixture in the Mandenka, but did find one divergent haplotype in some other West African groups, such as the Yoruba. This is consistent with what I mentioned earlier; West-Central Africa may have been populated relatively recently by Africans from other parts of Africa. The genetic archaic admixture found in the southerly West Africans could be a remnant of the recent humans with some archaic traits that were found in Nigeria. That would also explain the clear links of the Hofmeyr skull with Upper Paleolithic Eurasians, also from around the same age.

There is nothing surprising about the great similarity between Upper Paleolithic modern humans all over the world. This is consistent with the 70 kya OOA dispersal of modern humans.

Hammer et al. only looked for signs of admixture with hominins that were more divergent from modern humans than Neanderthals. There is much more work to be done.

I don't doubt there is more archaic admixture to be found; I've argued for that for year. The question is why this particular signal of admixture occurs much later than the postulated admixture with Neandertals.

If Homo sapiens had a 130 thousand year head start in Africa, you'd expect them to absorb archaic Africans long before they did so in Asia. But that is not what we actually observe: on the contrary archaic Africans persist in the anthropological record long after the demise of the Neandertals.

There is nothing surprising about the great similarity between Upper Paleolithic modern humans all over the world. This is consistent with the 70 kya OOA dispersal of modern humans.

What is surprising is that Hofmeyr shows no signs of affinity to recent Africans, whereas Upper Paleolithic Europeans are clearly related to recent Europeans.

I would also note that Hofmeyr is about half the age of 70ky, so it is consistent with a post-70ky movement of people into Africa, rather than a 70ky movement of people Out-of-Africa.

Which, once again argues for continuity between 100ka Asians and the later Upper Paleolithic, and is quite inconsistent with a descent of the UP from African populations (for which there is no archaeological evidence anyway).

I don't doubt there is more archaic admixture to be found; I've argued for that for year.

So where are the mtDNA traces of this archaic admixture, and by the way, do you believe that only Africans have archaic hominin admixture?

The question is why this particular signal of admixture occurs much later than the postulated admixture with Neandertals.

If Homo sapiens had a 130 thousand year head start in Africa, you'd expect them to absorb archaic Africans long before they did so in Asia. But that is not what we actually observe: on the contrary archaic Africans persist in the anthropological record long after the demise of the Neandertals.

I have explained this several times already. You have not presented any evidence that modern humans and archaic Africans coexisted for long in the first place. The archaeological record in West-Central Africa currently does not support a continuous modern human settlement that goes back 200,000 years. Shortly after the time period when we do find significant evidence for a continous modern human presence in West-Central Africa, the archaics become extinct.

Say the word when you can show that homo sapiens coexisted with archaics for a long period of time in any part of Africa. FYI (although this should be obvious to you), there is only evidence for a 200,000 year long settlement of modern humans in the Eastern and Southern parts of Africa.

So where are the mtDNA traces of this archaic admixture, and by the way, do you believe that only Africans have archaic hominin admixture?

I repeat: I don't see any particular reason to assign the deepest clades of the mtDNA phylogeny to anatomically modern humans, since Homo sapiens co-existed with archaic forms of humans during that time. I have no idea what the people who bore these lineages looked like.

The fact that out of two archaic hominins tested so far, modern human populations are differentially affiliated to both tells me that "archaic admixture" has been ubiquitous in our species. More such admixture will turn up by comparing full genomes of modern humans.

I have explained this several times already. You have not presented any evidence that modern humans and archaic Africans coexisted for long in the first place.

I can't present any such evidence, because I don't believe they co-existed for long. I believe that much of Africa was dominated by archaic Africans into the Upper Paleolithic.

The archaeological record in West-Central Africa currently does not support a continuous modern human settlement that goes back 200,000 years.

The question is: if modern humans originated in East Africa 195ky ago (the time of the Omo skull), then why did it take them 180-190 k years to replace the archaics in Central/West Africa (which is right next door) and a much shorter period of time to settle everywhere else and replace every other archaic hominin on the planet.

You can argue for African population structure. I've argued for such myself. The problem is why people who originated in East Africa made excursions to West Asia before 100ky and colonized every part of the Old World by 30-40ky, and you still find archaic humans next door in Africa down to the Holocene.

Say the word when you can show that homo sapiens coexisted with archaics for a long period of time in any part of Africa. FYI (although this should be obvious to you), there is only evidence for a 200,000 year long settlement of modern humans in the Eastern and Southern parts of Africa.

There is no evidence of modern humans 200,000 years ago in South Africa.

Also, there is no evidence for a 200,000 year long settlement of modern humans in East Africa. Rather, there is what is considered to be an early Homo sapiens skull in East Africa about 200,000 years (Omo I) ago, co-existing with a much more primitive skull (Omo II). There really is no case for continuity yet, since Herto is more primitive than Omo I, and later skulls from Africa such as Singa, Djebel Irhoud 1/2 and LH18 from Tanzania don't really cluster close to modern humans like a few of the Mount Carmel skulls do.

I repeat: I don't see any particular reason to assign the deepest clades of the mtDNA phylogeny to anatomically modern humans, since Homo sapiens co-existed with archaic forms of humans during that time. I have no idea what the people who bore these lineages looked like.

The fact that out of two archaic hominins tested so far, modern human populations are differentially affiliated to both tells me that "archaic admixture" has been ubiquitous in our species. More such admixture will turn up by comparing full genomes of modern humans.

From what I understand, based on your previous posts, you consider the mtDNA dating that has been done to be reliable. If so, what do you make of the dating of Mitochondrial Eve, which is close to the earliest finds of anatomically modern humans?

The mtDNA phylogeny shows the great diversity and continuous evolution of L(x L3) in Africa. I would like to know how you reconcile this with the belief that L3 is a modern human lineage, while L0 is supposedly from archaic hominins. And what in the world was the mtDNA of the pre-150 kya anatomically modern humans living in Africa, if you are ascribing L3 to the 100 kya Asians and the more divergent mtDNA haplogroups to archaics?

Not to mention that the divergent branches of the Y-DNA phylogeny are found most frequently in the populations where the most divergent branches of the mtDNA phylogeny are also most common, and these are also dated to the same general time period (>100 kya).

Furthermore, I have a hard time understanding how you can dismiss the possibility that mtDNA traces of archaic admixture in Eurasia and elsewhere could have been lost if you also believe that archaic admixture has been "ubiquitous" in our species.

"So, for example, X1 and X2 are dated at 21K and 22Kya, respectively, and X2a at 14.1 - with the origin of X1 and X2 postulated somewhere in the Near East/Caucasus region. Does anyone with a half-way intact mind really believe that these folks migrated from there into the Americas exactly during the height of the last ice age, also - neatly - not leaving any archeological nor genetic trace in between, and no autosomal or y-DNA connection, either?"

Whether or not it is the truth, it is defensible. The height of the last ice age is the moment at which the Beringian land bridge would have been widest. And, of course, the point in time at which a lineage originates can be much earlier than the time at which it migrates or expands. There are traces of X in Siberia. And, equally important we know of at least six waves of late/post-Paleolithic events that could have skewed modern population genetics in Siberia from whatever it was at that point (Uralic, Tocharian, Indo-Iranian, Turkic, Mongolian, Russian). The earliest modern human Siberians probably are at least as early as the Siberian megafauna extinction ca. 30kya, there was a population retreat at LGM, and a subsequent repopulation after, in addition to the six waves of more recent population shifts. The place of origin for X is pretty powerfuly argued by the fact that only the Druze (who now live in the Levant and according to their own legends have origins in the Taurus or Zargos Mountains) have both X1 and X2 at non-trivial frequency.

"I think back-migration into Africa is all but certain."

But when? The back-migration associated with M1/U6 looks like it dates to the Holocene, very likely Natufian. The Ethio-Semitic back-migration is probably Bronze Age. Madagascar is ca. 1000-2000 years ago, and the back-migration event that brought bannanas to African Bantus is more or less of the same era.

The case for pre-Holocene Upper Paleolithic back migration is much weaker, and it is at least as plausible that women with old L3 lineages migrated from East Africa to Arabia at a later date as the reverse. It could very well be that the old L3 lineages in Arabia are indeed the parallel lineages to M and N that never took off. But, the case that L3 itself had Arabian origins and then back migrated to East Africa is a very long shot given what we do know. It isn't absolutely impossible, but it isn't very parsimonious either.

"You are assuming that the entirety of the non-L3 part of the mtDNA phylogeny, going all the way back to mtDNA Eve, c. 200 thousand years ago was associated with anatomically modern humans. That assumption is unwarranted, since the African palaeoanthropological record shows an entire series of populations with a mix of archaic and modern traits down to a few thousand years ago."

The case for mtDNA Eve being modern human (or at least the slightly weaker proposition that all modern humans receive their mtDNA from a modern human who had the same or trivially mutated mtDNA from mtDNA Eve - obviously there is an archaic homo mtDNA lineage from which modern humans derive if you go back far enough) has a lot to be said for it. The date is just about right for a common modern human source, but is far too young for any known archaic species. The mtDNA phylogeny has extant modern human representatives at almost every step of the tree. The old Y-DNA lineages have a rough correspondence to the old mtDNA lineages (e.g. Y-DNA A and B basically correspond to the mtDNA L). Critically, the Neanderthals mtDNA is deeply divergent, so an introgressed mtDNA lineage would have to come from an archaic hominin that diverged from modern humans much more recently than Neanderthals. And, there are plausible admixture models that can explain an absence of Y-DNA and mtDNA lineages from archaics despite the presence of autosomoal DNA ancestry from archaics.

From what I understand, based on your previous posts, you consider the mtDNA dating that has been done to be reliable. If so, what do you make of the dating of Mitochondrial Eve, which is close to the earliest finds of anatomically modern humans?

As I said, 200 thousand years ago Homo sapiens was not the only species inhabiting Africa, so I don't have an opinion whether mtDNA Eve was an anatomically modern human. The same applies to any of her daughters and matrilineal descendants until such time as modern humans replaced archaic humans completely, in which case they would _have to be_ modern human.

The mtDNA phylogeny shows the great diversity and continuous evolution of L(x L3) in Africa. I would like to know how you reconcile this with the belief that L3 is a modern human lineage, while L0 is supposedly from archaic hominins.

I don't know if I understand your question. Clearly, all parts of the mtDNA phylogeny came to be associated with Homo sapiens. They all exist in extant humans who all belong to the species Homo sapiens.

The question is whether they have all, always, existed within Homo sapiens. Since I think that there was gene flow between modern and archaic humans in Africa, and these two groups co-existed until fairly recently in geological terms, I can't really tell whether mtDNA Eve, or any of her matrilineal descendants were Homo sapiens, Homo something else, or a mix between the two.

What we do know is that they all ultimately came to be associated with modern humans.

In the case of L3, it is likely that it was always associated with modern humans, since it is of a similar age to M and N, and, modern humans must have carried those because the archaic Eurasians seem to have carried completely unrelated mtDNA lineages as far as we can tell.

Not to mention that the divergent branches of the Y-DNA phylogeny are found most frequently in the populations where the most divergent branches of the mtDNA phylogeny are also most common, and these are also dated to the same general time period (>100 kya).

That is not the case. The most divergent branches of the Y-DNA phylogeny are found in West/North Africa, as the recent re-drawing of the phylogeny has shown; of the mtDNA phylogeny in East/South Africa apparently.

Furthermore, I have a hard time understanding how you can dismiss the possibility that mtDNA traces of archaic admixture in Eurasia and elsewhere could have been lost if you also believe that archaic admixture has been "ubiquitous" in our species.

There was much less opportunity to mix with archaics in Eurasia. Most of Eurasia was colonized during the Upper Paleolithic by bearers of an advanced technology that managed to drive to extinction all pre-existing hominins within a few thousand years.

I do think Eurasians may have some Neandertal admixture, albeit at much smaller levels than 4%, since that figure is based on genomewide comparisons that ignore the absorption of archaics in Africa, in addition to ignoring modern human admixture in Neandertals. If there was only, say, 0.5-1% Neandertal admixture, then it is much easier to imagine any mtDNA contributions coming from Neandertals being lost due to drift.

Critically, the Neanderthals mtDNA is deeply divergent, so an introgressed mtDNA lineage would have to come from an archaic hominin that diverged from modern humans much more recently than Neanderthals.

We have two samples (Neandertals and Denisovans) that are about equidistant to humans autosomally, but carry mtDNA that is about 500,000 years apart in terms of time depth.

So, I see no reason to think that any particular level of mtDNA divergence should accompany any particular level of autosomal (let alone morphological) divergence.

"I do think Eurasians may have some Neandertal admixture, albeit at much smaller levels than 4%, since that figure is based on . . . ignoring modern human admixture in Neandertals."

This is a quite plausible point, although I am less convinced of the loss of mtDNA due to genetic drift or the invalidity of estimates based on comparisons to Africans who are also archaic admixed (I see the theory for the latter, but given that the comparison is to West African Yoruba, rather than Khoisans or Pygmies where there is more evidence of archaic admixture, I'm not sure that I buy it - the Yoruba probably have any of their archaic admixture in common with Eurasians and pre-dating Out of Africa, so the methodology should work.)

The Neanderthal DNA samples we have post-date Neanderthal-modern human encounters, it is highly plausible that the gene exchange went both ways, and in a naiive direct comparison, modern human specific genes that introgress into Neanderthals look like Neanderthal DNA in modern humans if you assume that the Neanderthal DNA had no modern human introgression. Also, it isn't unreasonable to interpret late Neanderthal technological innovatioon as a product of admixture from modern humans.

Now, linkage and recombination patterns in the genome ought to be able in theory at least to distinguish between introgressed modern human genes seen in Neanderthals and true Neanderthal genes, but that rests of some very subtle statistical analysis.

For Saudi Arabia to be source of West Eurasian genes, it needs to have the root DNAs of both M and N haplogroups. All the basal lineages of M and N are located in India. Arabia never had the natural resource to generate a population expansion (or population explosion) to have caused migration outside in sufficient numbers to colonize a whole continent. We should never ignore the ecological factors.

The population of India is the result of relatively recent admixture. Also, the climate of Arabia (and by "Arabia" I also include the now-submerged lands of the Gulf) has not been constant, and there were periods favoring human occupation followed by periods that didn't. Actually that makes it such an attractive source of population expansion, since population could have grown in the good times, and dispersed during the bad times.

The Neanderthal DNA samples we have post-date Neanderthal-modern human encounters, it is highly plausible that the gene exchange went both ways, and in a naiive direct comparison, modern human specific genes that introgress into Neanderthals look like Neanderthal DNA in modern humans if you assume that the Neanderthal DNA had no modern human introgression. Also, it isn't unreasonable to interpret late Neanderthal technological innovatioon as a product of admixture from modern humans.

The recent discovery that Vindija is an atypical Neandertal that is close to modern humans strengthens the case for modern-to-Neandertal introgression.

"The recent discovery that Vindija is an atypical Neandertal that is close to modern humans strengthens the case for modern-to-Neandertal introgression."

Agreed. There is suggstive evidence from both bones and stones that late Neanderthals may have had modern human admixture, although the evidence isn't conclusive either in isolation or even taken together. You really need genetic linkage analysis to really have conclusive evidence, and given the incomplete nature of the Neanderthal genome that is much harder to marshal on he Neanderthal side than the modern human side.

So, what you really need is evidence of Neanderthal gene matches that don't show genetic linkage patterns consistent with introgression in the human genome - and that too is tricky, because 30,000 years of recombination blurs that signal.

"The earliest modern human Siberians probably are at least as early as the Siberian megafauna extinction ca. 30kya, there was a population retreat at LGM, and a subsequent repopulation after, in addition to the six waves of more recent population shifts".

And I believe that explains the absence of mt-DNA N haplogroups through much of the region they must have migrated through on their way to SE Asia and Australia. It is difficult to argue a case from mt-DNA N having migrated east through South Asia. We would be left then with vanishing haplogroups in a region where a huge diversity of haplogroups has survived.

"I would like to know how you reconcile this with the belief that L3 is a modern human lineage, while L0 is supposedly from archaic hominins".

Mitochondrial DNA does not always coincide even with 'species'. For example European bison have mt-DNA lineages closely related to those of cattle but American bison have distinct mt-DNA lineages. And mt-DNA of dabbling ducks is all over the place. It is therefore quite possible that the mt-DNA remained as the population in Africa moved towards 'modernity', whatever that means. But, of course, that makes it more difficult to explain the absence of non-African 'archaic' haplogroups. Although:

"there are plausible admixture models that can explain an absence of Y-DNA and mtDNA lineages from archaics despite the presence of autosomoal DNA ancestry from archaics".

Yes. Shifts in culture or technology can explain such, but then the problem becomes how did pre-modern haplogroups survive in Africa?

"it is at least as plausible that women with old L3 lineages migrated from East Africa to Arabia at a later date as the reverse".

Here are some comments I made at Maju's blog. Of course he absolutely refuses to accept the findings. They don't fit with what he wants to believe:

"We show that haplogroups N1 and N2, as well as haplogroup X, are ancient relicts of the dispersal of modern humans from Africa 160 ka ago and can provide insight into the earliest stages of the process".

The authors do seem to make the mistake of calling both N1 and N5 basal N haplogroups. This is presumably to make the evidence fit the fashionable 'southern' migration:

"they are most likely relicts from the first modern-human settlement in Arabia during the earliest stage of the southern coastal dispersal from the Horn of Africa to the rest of the world".

But they later say:

"In Southern Asia, only one new extant N(xR) branch, N5, arose; N5 is extremely rare and has also been recently described in Iran, raising the possibility that this lineage could also have arisen in Southwest Asia".

Interesting. That seems to wipe out any 'via India' route, unless you're going to stick with R in South Asia. On that subject the authors say:

"This suggests that haplogroup N had an origin immediately outside Africa, most likely in the Arabian Peninsula. This region was probably also the cradle for haplogroup R, dating to 159 ka ago".

So they have R originating in SW Asia as well. But the study does not include R so their claim is not well-supported here.

"Other N(xR) haplogroups include N5 in Southern Asia, N9 and A in Eastern Asia, N21 and N22 in Southeast Asia, and O and S in Australasia".

For a start N13 and N14 (which they leave out) along with O and S are confined to the 'Australian' portion of Australasia. And the authors don't mention N8, N10 or N11 either, all South Chinese. And N5 is part of N1'5. Of course I agree with this statement:

"Strictly speaking, haplogroups N and R could have arisen anywhere in the region between Southwest Asia and Australasia; basal branches are found in this region today. However, given L3's genesis in eastern Africa, the most parsimonious location for their origin is in the vicinity of the Arabian Peninsula".

That has long been my position. In summary:

"Whereas distinct episodes of dispersal and expansion into and within Europe (and indeed America) can be detected, demographic expansion in Southwest Asia appears as a continuous phenomenon from the Late Glacial period through to the Neolithic period. This genetic evidence is consistent with archaeological interpretations of the expansion of sedentary Natufian hamlets in the Levant during the wet phase between 15 and 13 ka ago. Such expansion lead to the techniques of agriculture and domestication under the harsher conditions of the Younger Dryas and ultimately to the Neolithic cultures of the early Holocene"

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